The triplet specificities and required strand orientations of two classes of DNA triple helices can be combined to double helical sequences containing all four base pairs by alternate strand triple helix formation. This allows for the of oligonucleotides containing only natural 3'-5' phosphodiester linkages to simultaneously bind both strands of double DNA in the major groove. The stabilities and structures of these alternate strand triple helices depend on whether binding site sequence is 5'-(purine)_m(pyrimidine)_n-3' or 5'-(pyrimidine)_m(purine)_n-3'. The sequence type 5'-(purine)_m-(pyrimidine)_n-3' was targeted with an oligonucleotide consisting of a pyrimidine domain and a purine domain linked by a 3'-5' . To bind the duplex sequence type 5'-(pyrimidine)_m(purine)_n-3', the third strand requires at least two nucleotides binding domains at the site of crossover in the major groove. A new class of oligonucleotides capable of binding mixed sequences by crossovers in the major groove may be possible.
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Beal et al. (1992) studied this question.